TABLE 3.
Catabolism-related genes showing twofold or greater pH dependence (pH 6.0/pH 9.0 expression ratios)
| Gene(s) | Characteristics | Reaction or pathway (known or putative) |
|---|---|---|
| Acid-upregulated | ||
| adhA | Alcohol dehydrogenase | Alcohol + NADP+ ⇌ aldehyde + NADPH |
| ald | l-Alanine dehydrogenase | Alanine + NAD+ ⇌ pyruvate + NADH + NH4+ |
| alsDS, ilvH | 2-Acetolactate synthase, 2-acetolactate decarboxylase | Pyruvate → acetolactate + CO2 → acetoin + 2CO2 |
| cypE | NADPH-cytochrome P450 reductase | ETS |
| fdhD, yjgC, yrhE, and yrhG | Formate dehydrogenase homologs | HCO2− + NAD+ → CO2 + NADH |
| gabD | Succinate-semialdehyde dehydrogenase | Succinic semialdehyde + glutamate → succinate |
| gcvPA | Probable glycine decarboxylase | Glycine + H-protein-lipoyllysine → H-protein-S-aminomethyldihydrolipoyllysine + CO2 |
| hxlA, hxlB, hxlR | 3-Hexulose 6-phosphate synthase | d-Ribulose 5-phosphate + formaldehyde ⇌ d-arabino-3-hexulose 6-phosphate |
| maeA | Malate decarboxylase homolog | Malate + NAD+ → pyruvate + NADH + CO2 |
| psd, pssA | Phosphatidylserine decarboxylase | CDP-diacylglycerol + l-serine → l-1-phosphatidyl-ethanolamine + CO2 + CMP |
| speA | Arginine decarboxylase | Arginine → agmatine + CO2 |
| ycdF, ycdG | Glucose 1-dehydrogenase and oligo-1,6-glucosidase homologs | d-Glucose + NAD(P)+ → d-glucono-1,5-lactone + NAD(P)H |
| ydaD | Alcohol dehydrogenase homolog | Alcohol + NAD(P)+ → aldehyde + NAD(P)H + H+ |
| ytbE | Plant metabolite dehydrogenase homolog | |
| yvfV | Glycolate oxidase homolog | Glycolate → glyoxylate |
| Base-upregulated | ||
| acuABC | Acetoin dehydrogenase | 2-Acetolactate → acetoin + CO2 |
| amyX, bglS | Pullulanase and glucanase | Glucan catabolism |
| atpA, atpC, atpD, atpI | ATP synthase | H+(out) + P + ADP = H+(in) + H2O + ATP |
| azoR2 | NAD(P)H dehydrogenase (quinone) homolog | ETS |
| ctaA, ctaC, ctaD, ctaE, ctaF | Cytochrome caa3 oxidase | ETS |
| cydABCD | Cytochrome bd ubiquinol oxidase | ETS |
| fruA, fruB | Fructose l-phosphate kinase | Glycolysis |
| gltAB | Glutamate synthase | l-Glutamine + α-ketoglutarate → 2 l-glutamate |
| idh, iolB, iolD, iolH, iolI | myo-Inositol catabolism | myo-Inositol → dihydroxyacetone phosphate + acetyl-coenzyme A + CO2 |
| lacA | Beta-galactosidase | Lactose → β-d-glucose + β-d-galactose |
| ldh, lctP | l-Lactate dehydrogenase, permease | Pyruvate → l-lactate |
| mccA, mccB | Methionine catabolism to cysteine | Methionine → cysteine → pyruvate |
| mmgD | Propionyl-coenzyme A metabolism | Propionyl-coenzyme A → succinate (trichloroacetic acid cycle) |
| narG, narH, narI | Nitrate reductase | 2 Nitrate → 2 nitrite → N2 |
| rocA, rocB, rocDEF, rocG | Arginine catabolism | l-Arginine → l-glutamate + 2NH4+ |
| treA, treP | Trehalose-6-phosphate hydrolase | Trehalose catabolism |
| xlyA, xhlA, xhlB | N-Acetylmuramoyl-l-alanine amidase; cell wall lysis | Peptidoglycan catabolism |
| ybcF | Carbonic anhydrase homolog | CO2 + H2O → HCO3− + H+ |
| ydbM | Butyryl-CoA dehydrogenase homolog | Butyrate catabolism |
| yisK | Pentene tricarboxylic acid decarboxylase homolog | |
| yrbE | Oxidoreductase homolog |